Sorry to drag this out of the depths of the General Discussion, but I just discovered this thread and I think this project deserves to live on!
I wish I had box scans I could contribute, but I thought I'd at least try to tack a whack at the SNES controller box using the scans provided earlier in this discussion. I'm not experienced at making more than PC covers, so I'm doing my best at creating it for the vertical SNES template. I also tracked down better images of Yoshi and Mario from Mario RPG. Of course it would be ideal if someone had better quality scans, but I can at least make something until then. Here's a preview of the front so far:

If there's any chance of this project continuing, I'd personally love to see a cover for the green Gameboy Color (if it fits in a UGC, or whatever works). My original one I grew up playing with was stolen long ago, but today I just got a practically new one, which is pretty exciting! I'd also love so see one for GBA and GBA SP eventually. If anyone out there has the boxes to scan, I'll even take a shot at them myself.